Open Access Highly Accessed Research article

Whole genome analysis of p38 SAPK-mediated gene expression upon stress

Isabel Ferreiro1, Manel Joaquin1, Abul Islam2, Gonzalo Gomez-Lopez3, Montserrat Barragan1, Luís Lombardía4, Orlando Domínguez5, David G Pisano3, Nuria Lopez-Bigas2, Angel R Nebreda6* and Francesc Posas1*

Author Affiliations

1 Cell Signaling Unit, Universitat Pompeu Fabra (UPF) Dr aiguader 88, Barcelona 08003, Spain

2 Research Unit on Biomedical Informatics. Departament de Ciències Experimentals i de la Salut (DCEXS), Universitat Pompeu Fabra (UPF) Dr aiguader 88, Barcelona 08003, Spain

3 Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

4 Molecular Diagnostics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

5 Genomics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

6 Signalling and Cell Cycle Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

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BMC Genomics 2010, 11:144  doi:10.1186/1471-2164-11-144

Published: 1 March 2010

Additional files

Additional file 1:

Pearson correlation coefficient analysis (PCC). Correlation between the two replicates was analyzed by PCC as described in methods. All samples showed very high correlation coefficient with most correlation values higher than 0.9, which indicates high fidelity of the experimental biological replicates.

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Additional file 2:

Microarray Quality Metrics Analysis. For a better visualization the microarray data the diagnosis has been split in three groups named 1; Treatment and Time Course. 2; p38α SAPK knock out MEFs and 3; SB203580 treated wildt type MEFs. Section 1 analyses the individual array quality through MA. The mass distribution in an MA plot is expected to be concentrated along the M = 0 axis and there should be no trend in the mean of M as a function of A. A trend in the lower range of A usually indicates that the arrays have different background intensities. A trend in the upper range of A usually indicates saturation of the measurements. Section 2 analyses the array intensity distributions through Box plots and Density plots. Each Box box corresponds to one array. Array duplicates are shown side by side. The left panel corresponds to the red Cy5 channel. The middle panel corresponds to the green Cy3 channel. The right panel shows the Box plots of the log2 Cy5/Cy3 ratio. Box plots are a graphical representation that summarises the distribution of probe intensities across all arrays. It comprises the smallest observation, lower quartile, median, upper quartile and largest observation. All boxes are expected to have similar size and median. Density plots show smoothed histograms of the array signal intensities. The left panel corresponds to the red Cy5 channel. The middle panel corresponds to the green Cy3 channel. The right panel shows the Box plots of the log2 Cy5/Cy3 ratio. The distribution of the arrays is expected to have similar shapes and ranges.

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Additional file 3:

2.5-fold up-regulated genes upon transient p38 SAPK activation. List of unique Ensemble-Id genes up-regulated 2.5 fold over a pool of control cells upon a transient p38 SAPK activation. Wild type MEFs and p38α-/- knock out MEFs cells were stimulated with 100 ng/ml TNFα, 25 ng/ml anisomycin and 100 mM NaCl for the indicated times in the absence or presence of 10 μM of SB203580. The p38 SAPK dependent genes are highlighted.

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Additional file 4:

4-fold down-regulated genes upon transient p38 SAPK activation. List of unique Ensemble-Id genes down-regulated 2.5 fold over a pool of control cells upon a transient p38 SAPK activation. Wild type MEFs and p38α-/- knock out MEFs cells were stimulated with 100 ng/ml TNFα, 25 ng/ml anisomycin and 100 mM NaCl for the indicated times in the absence or presence of 10 μM of SB203580. The p38 SAPK dependent genes are highlighted.

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Additional file 5:

GO statistic analysis. Statistics showing significant (p-value ≤ 0.05 and multiple test corrected p-value) in the GO cell component, molecular function and biological processes enriched by the treatments NaCl, anisomycin and TNFα. Total observed genes and total gene number in a given category is also shown.

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Additional file 6:

GO analysis miniweb. Interactive miniweb showing the treatment and NaCl time course GO analysis with access to the up-regulated genes found in every category. Files can be open with any standard web browser.

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Additional file 7:

Supplementary figure 1: The TNFα gene network. The TNFα gene network inferred by the Ingenuity Pathway software is related to the control of the Immune Response and Immunological Disease. The network genes shaded in grey are up-regulated by the treatment. The network genes in white are not up-regulated by the treatment. Solid arrows indicate direct interactions. Broken arrows indicate indirect interactions.

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Additional file 8:

Supplementary figure 2: The anisomycin gene network. The anisomycin gene network inferred by the Ingenuity Pathway software is related to the control of Cell Development and Gene Expression.

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Additional file 9:

Supplementary figure 3: The NaCl (2 h) gene network. The NaCl gene network at 2 h inferred by the Ingenuity Pathway software is related to the control of Cell Cycle and Post-translational Modification.

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Additional file 10:

Supplementary figure 4: The common response gene network. The common response gene network inferred by the Ingenuity Pathway software is related to the control of Gene Expression and Cancer.

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